Ocean and Ecosystem Science Seminar Series | BIO | 2019-11-06

Background

The greatest value of a picture is when it forces us to notice
what we never expected to see.
   - Tukey (1977)

  • Discovery is one of the most exciting parts of science
  • Visualizations are one of the tools we use to reveal patterns
  • Models allow us to simplify and describe these patterns
  • At various stages, we need to communicate our findings

Communicating information

Simplified workflow:

Data


\(\rightarrow\)

Models


\(\rightarrow\)

Discuss

  • Connections may not come easy
    • Growing volume and variety of data
    • Increasingly complex models
    • Diverse backgrounds

Stock assessments

  • Communicating stock assessment results isn’t getting easier
    • Growing volume and variate of data
    • Increasingly complex models
    • Diverse backgrounds
  • Traditional formats sometimes
    • Overwhelm participants with endless tables and figures
    • Fail to convey the richness of information available

Interactive tools

  • Simplify communication and improve accessibility
  • Common tools that are used daily on a range of websites
  • Their use is no longer restricted to website developers
    • Integrated into software commonly used by the research community
    • Surprisingly easy to generate interactive dashboards
    • Growing number of users

Objective

  • Using examples we aim to demonstrate that interactive tools can simplify our workflow, from data and model exploration to communication
  • Examples:
    1. RStrap Explorer: A tool for examinging fishery-independent survey data
    2. Tag Explorer: A mapping tool developed for the exploration of a long-term tagging study
    3. NCAM Explorer: A tool for exploring results from the Northern Cod Assessment Model

RStrap Explorer

  • Fisheries-independent surveys have become a mainstay in stock assessment
  • Stratified-random surveys have been conducted by DFO for > 40 years
  • Typically analyzed using stratified analyses (RStrap in NL region)



  Canadian Coast Guard | Twitter

RStrap Explorer

  • Running a series of stratified analysis can be cumbersome
library(Rstrap)

## Load survey data
load("converted_set_details_2017-04-27.Rdata")
load("converted_length-frequency_data_2017-04-27.Rdata")
load("age-growth_data_2017-04-27.Rdata")

## 3NO Witch Flounder
witch <- strat.fun(setdet = setdet, data.series = "Campelen", 
                   species = 890, survey.year = 1995:2012, 
                   season = "spring", NAFOdiv = c("3N", "3O"))

## 3K Roughhead Grenadier (length disaggregated)
grenadier <- strat.fun(setdet = setdet, lf = lf, data.series = "Campelen", 
                       program = "strat2 & strat1", species = 474, survey.year = 2012, 
                       season = "fall", NAFOdiv = "3K", strat = 622:654, sex = "unsexed", 
                       length.group = 0.5, group.by = "length")

## 2J3KL Greenland Halibut (length and age disaggregated)
turbot <- strat.fun(setdet = setdet, lf = lf, ag = ag, data.series = "Campelen", 
                    program = "strat2 & strat1", species = 892, survey.year = 1998:2012, 
                    season = "fall", NAFOdiv = c("2J", "3K", "3L"), 
                    sex = c("male","female","unsexed"), length.group = 1, 
                    group.by = "length & age")

## 3Ps Atlantic Cod (length and age disaggregated)
cod <- strat.fun(setdet = setdet, lf = lf, ag = ag, data.series = "Campelen", 
                 program = "strat2 & strat1", species = 438, survey.year = 1998:2012, 
                 season = "spring", NAFOdiv = "3P", sex = c("male","female","unsexed"), 
                 length.group = 1, group.by = "length & age")
  • This doesn’t include code for plotting these results

RStrap Explorer

  • A dashboard was created using the shiny, flexdashboard, plotly, and crosstalk packages to dynamically run and explore RStrap results
  • Four primary pages:
    1. Survey Indices contains stock level estimates of biomass and abundance
    2. Age & Length Distributions contains length and age frequency plots
    3. Recruitment displays recruitment indices
    4. Help provides additional context to the survey data and analysis

RStrap Explorer

RStrap Explorer

Tag Explorer

  • For some data-rich stocks, mark and recapture studies are carried out to estimate movement, growth rate, natural mortality, etc.
  • There is a long-standing tagging program for Northern cod
    • >60 years, >60,000 records, 1,000 - 10,000 tags deployed annually

Photo: John Brattey

Tag Explorer

  • Spatial explorations of these data have been limited since the seminal work by Taggart et al. 1995

  • Nearly 500 pages!

Tag Explorer

  • A dashboard was created using the shiny, shinydashboard, and leaflet packages to dynamically explore this large dataset
  • Contains
    • One primary page, Main map, where release and recovery locations are mapped
    • A series of summary pages where these data are summarised

Tag Explorer

Tag Explorer